PMC:7443692 / 41566-43034 JSONTXT

{"project":"LitCovid-sample-MedDRA","denotations":[{"id":"T13","span":{"begin":727,"end":750},"obj":"http://purl.bioontology.org/ontology/MEDDRA/10022891"}],"attributes":[{"id":"A13","pred":"meddra_id","subj":"T13","obj":"http://purl.bioontology.org/ontology/MEDDRA/10058063"}],"text":"Several emerging variants of the virus appear to be altering N-linked glycosylation occupancy by disrupting N-linked sequons. Interestingly, the two N-linked sequons in SARS-CoV-2 S directly impacted by variants, N0074 and N0149, are in divergent insert regions 1 and 2, respectively, of SARS-CoV-2 S in comparison with SARS-CoV-1 S (Figure 4A). The N0074, in particular, is one of the S glycans that interact directly with ACE2 glycan (at N546; Figure 7), suggesting that glycan-glycan interactions could contribute to the unique infectivity differences between SARS-CoV-2 and SARS-CoV-1. These sequon variants will also be important to examine in terms of glycan shielding that could influence immunogenicity and efficacy of neutralizing antibodies, as well as interactions with the host cell receptor ACE2. Naturally occurring amino acid-changing SNPs in the ACE2 gene generate a number of variants including one variant, with a frequency of three in 10,000 humans, that eliminates a site of N-linked glycosylation at N546 (Figure 6). Understanding the impact of ACE2 variants on glycosylation and more importantly on S binding, especially for N546S, which impacts the glycan-glycan interaction between S and ACE2 (Figure 7), should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation could lead to more potent biologics capable of acting as better competitive inhibitors of S binding."}

{"project":"LitCovid-sample-CHEBI","denotations":[{"id":"T227","span":{"begin":388,"end":395},"obj":"Chemical"},{"id":"T228","span":{"begin":830,"end":840},"obj":"Chemical"}],"attributes":[{"id":"A227","pred":"chebi_id","subj":"T227","obj":"http://purl.obolibrary.org/obo/CHEBI_18154"},{"id":"A228","pred":"chebi_id","subj":"T228","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"}],"text":"Several emerging variants of the virus appear to be altering N-linked glycosylation occupancy by disrupting N-linked sequons. Interestingly, the two N-linked sequons in SARS-CoV-2 S directly impacted by variants, N0074 and N0149, are in divergent insert regions 1 and 2, respectively, of SARS-CoV-2 S in comparison with SARS-CoV-1 S (Figure 4A). The N0074, in particular, is one of the S glycans that interact directly with ACE2 glycan (at N546; Figure 7), suggesting that glycan-glycan interactions could contribute to the unique infectivity differences between SARS-CoV-2 and SARS-CoV-1. These sequon variants will also be important to examine in terms of glycan shielding that could influence immunogenicity and efficacy of neutralizing antibodies, as well as interactions with the host cell receptor ACE2. Naturally occurring amino acid-changing SNPs in the ACE2 gene generate a number of variants including one variant, with a frequency of three in 10,000 humans, that eliminates a site of N-linked glycosylation at N546 (Figure 6). Understanding the impact of ACE2 variants on glycosylation and more importantly on S binding, especially for N546S, which impacts the glycan-glycan interaction between S and ACE2 (Figure 7), should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation could lead to more potent biologics capable of acting as better competitive inhibitors of S binding."}

{"project":"LitCovid-sample-PD-NCBITaxon","denotations":[{"id":"T108","span":{"begin":169,"end":179},"obj":"Species"},{"id":"T109","span":{"begin":288,"end":298},"obj":"Species"},{"id":"T110","span":{"begin":320,"end":328},"obj":"Species"},{"id":"T111","span":{"begin":563,"end":573},"obj":"Species"},{"id":"T112","span":{"begin":578,"end":586},"obj":"Species"},{"id":"T113","span":{"begin":961,"end":967},"obj":"Species"}],"attributes":[{"id":"A108","pred":"ncbi_taxonomy_id","subj":"T108","obj":"NCBItxid:2697049"},{"id":"A109","pred":"ncbi_taxonomy_id","subj":"T109","obj":"NCBItxid:2697049"},{"id":"A110","pred":"ncbi_taxonomy_id","subj":"T110","obj":"NCBItxid:694009"},{"id":"A111","pred":"ncbi_taxonomy_id","subj":"T111","obj":"NCBItxid:2697049"},{"id":"A112","pred":"ncbi_taxonomy_id","subj":"T112","obj":"NCBItxid:694009"},{"id":"A113","pred":"ncbi_taxonomy_id","subj":"T113","obj":"NCBItxid:9605"}],"namespaces":[{"prefix":"NCBItxid","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"text":"Several emerging variants of the virus appear to be altering N-linked glycosylation occupancy by disrupting N-linked sequons. Interestingly, the two N-linked sequons in SARS-CoV-2 S directly impacted by variants, N0074 and N0149, are in divergent insert regions 1 and 2, respectively, of SARS-CoV-2 S in comparison with SARS-CoV-1 S (Figure 4A). The N0074, in particular, is one of the S glycans that interact directly with ACE2 glycan (at N546; Figure 7), suggesting that glycan-glycan interactions could contribute to the unique infectivity differences between SARS-CoV-2 and SARS-CoV-1. These sequon variants will also be important to examine in terms of glycan shielding that could influence immunogenicity and efficacy of neutralizing antibodies, as well as interactions with the host cell receptor ACE2. Naturally occurring amino acid-changing SNPs in the ACE2 gene generate a number of variants including one variant, with a frequency of three in 10,000 humans, that eliminates a site of N-linked glycosylation at N546 (Figure 6). Understanding the impact of ACE2 variants on glycosylation and more importantly on S binding, especially for N546S, which impacts the glycan-glycan interaction between S and ACE2 (Figure 7), should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation could lead to more potent biologics capable of acting as better competitive inhibitors of S binding."}

{"project":"LitCovid-sample-sentences","denotations":[{"id":"T251","span":{"begin":0,"end":125},"obj":"Sentence"},{"id":"T252","span":{"begin":126,"end":345},"obj":"Sentence"},{"id":"T253","span":{"begin":346,"end":589},"obj":"Sentence"},{"id":"T254","span":{"begin":590,"end":809},"obj":"Sentence"},{"id":"T255","span":{"begin":810,"end":1037},"obj":"Sentence"},{"id":"T256","span":{"begin":1038,"end":1320},"obj":"Sentence"},{"id":"T257","span":{"begin":1321,"end":1468},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Several emerging variants of the virus appear to be altering N-linked glycosylation occupancy by disrupting N-linked sequons. Interestingly, the two N-linked sequons in SARS-CoV-2 S directly impacted by variants, N0074 and N0149, are in divergent insert regions 1 and 2, respectively, of SARS-CoV-2 S in comparison with SARS-CoV-1 S (Figure 4A). The N0074, in particular, is one of the S glycans that interact directly with ACE2 glycan (at N546; Figure 7), suggesting that glycan-glycan interactions could contribute to the unique infectivity differences between SARS-CoV-2 and SARS-CoV-1. These sequon variants will also be important to examine in terms of glycan shielding that could influence immunogenicity and efficacy of neutralizing antibodies, as well as interactions with the host cell receptor ACE2. Naturally occurring amino acid-changing SNPs in the ACE2 gene generate a number of variants including one variant, with a frequency of three in 10,000 humans, that eliminates a site of N-linked glycosylation at N546 (Figure 6). Understanding the impact of ACE2 variants on glycosylation and more importantly on S binding, especially for N546S, which impacts the glycan-glycan interaction between S and ACE2 (Figure 7), should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation could lead to more potent biologics capable of acting as better competitive inhibitors of S binding."}

{"project":"LitCovid-sample-PD-MONDO","denotations":[{"id":"T68","span":{"begin":169,"end":179},"obj":"Disease"},{"id":"T69","span":{"begin":288,"end":298},"obj":"Disease"},{"id":"T70","span":{"begin":320,"end":328},"obj":"Disease"},{"id":"T71","span":{"begin":563,"end":573},"obj":"Disease"},{"id":"T72","span":{"begin":578,"end":586},"obj":"Disease"}],"attributes":[{"id":"A68","pred":"mondo_id","subj":"T68","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A69","pred":"mondo_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A70","pred":"mondo_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A71","pred":"mondo_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A72","pred":"mondo_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Several emerging variants of the virus appear to be altering N-linked glycosylation occupancy by disrupting N-linked sequons. Interestingly, the two N-linked sequons in SARS-CoV-2 S directly impacted by variants, N0074 and N0149, are in divergent insert regions 1 and 2, respectively, of SARS-CoV-2 S in comparison with SARS-CoV-1 S (Figure 4A). The N0074, in particular, is one of the S glycans that interact directly with ACE2 glycan (at N546; Figure 7), suggesting that glycan-glycan interactions could contribute to the unique infectivity differences between SARS-CoV-2 and SARS-CoV-1. These sequon variants will also be important to examine in terms of glycan shielding that could influence immunogenicity and efficacy of neutralizing antibodies, as well as interactions with the host cell receptor ACE2. Naturally occurring amino acid-changing SNPs in the ACE2 gene generate a number of variants including one variant, with a frequency of three in 10,000 humans, that eliminates a site of N-linked glycosylation at N546 (Figure 6). Understanding the impact of ACE2 variants on glycosylation and more importantly on S binding, especially for N546S, which impacts the glycan-glycan interaction between S and ACE2 (Figure 7), should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation could lead to more potent biologics capable of acting as better competitive inhibitors of S binding."}

{"project":"LitCovid-sample-UniProt","denotations":[{"id":"T2931","span":{"begin":424,"end":428},"obj":"Protein"},{"id":"T2932","span":{"begin":804,"end":808},"obj":"Protein"},{"id":"T2933","span":{"begin":862,"end":866},"obj":"Protein"},{"id":"T2934","span":{"begin":1066,"end":1070},"obj":"Protein"},{"id":"T2935","span":{"begin":1212,"end":1216},"obj":"Protein"},{"id":"T2936","span":{"begin":1282,"end":1286},"obj":"Protein"},{"id":"T2937","span":{"begin":1349,"end":1353},"obj":"Protein"}],"attributes":[{"id":"A2931","pred":"uniprot_id","subj":"T2931","obj":"https://www.uniprot.org/uniprot/Q9UFZ6"},{"id":"A2932","pred":"uniprot_id","subj":"T2932","obj":"https://www.uniprot.org/uniprot/Q9UFZ6"},{"id":"A2933","pred":"uniprot_id","subj":"T2933","obj":"https://www.uniprot.org/uniprot/Q9UFZ6"},{"id":"A2934","pred":"uniprot_id","subj":"T2934","obj":"https://www.uniprot.org/uniprot/Q9UFZ6"},{"id":"A2935","pred":"uniprot_id","subj":"T2935","obj":"https://www.uniprot.org/uniprot/Q9UFZ6"},{"id":"A2936","pred":"uniprot_id","subj":"T2936","obj":"https://www.uniprot.org/uniprot/Q9UFZ6"},{"id":"A2937","pred":"uniprot_id","subj":"T2937","obj":"https://www.uniprot.org/uniprot/Q9UFZ6"}],"text":"Several emerging variants of the virus appear to be altering N-linked glycosylation occupancy by disrupting N-linked sequons. Interestingly, the two N-linked sequons in SARS-CoV-2 S directly impacted by variants, N0074 and N0149, are in divergent insert regions 1 and 2, respectively, of SARS-CoV-2 S in comparison with SARS-CoV-1 S (Figure 4A). The N0074, in particular, is one of the S glycans that interact directly with ACE2 glycan (at N546; Figure 7), suggesting that glycan-glycan interactions could contribute to the unique infectivity differences between SARS-CoV-2 and SARS-CoV-1. These sequon variants will also be important to examine in terms of glycan shielding that could influence immunogenicity and efficacy of neutralizing antibodies, as well as interactions with the host cell receptor ACE2. Naturally occurring amino acid-changing SNPs in the ACE2 gene generate a number of variants including one variant, with a frequency of three in 10,000 humans, that eliminates a site of N-linked glycosylation at N546 (Figure 6). Understanding the impact of ACE2 variants on glycosylation and more importantly on S binding, especially for N546S, which impacts the glycan-glycan interaction between S and ACE2 (Figure 7), should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation could lead to more potent biologics capable of acting as better competitive inhibitors of S binding."}

{"project":"LitCovid-sample-PD-IDO","denotations":[{"id":"T119","span":{"begin":33,"end":38},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T120","span":{"begin":531,"end":542},"obj":"http://purl.obolibrary.org/obo/IDO_0000464"},{"id":"T121","span":{"begin":785,"end":789},"obj":"http://purl.obolibrary.org/obo/IDO_0000531"},{"id":"T122","span":{"begin":790,"end":794},"obj":"http://purl.obolibrary.org/obo/CL_0000000"},{"id":"T123","span":{"begin":987,"end":991},"obj":"http://purl.obolibrary.org/obo/BFO_0000029"}],"text":"Several emerging variants of the virus appear to be altering N-linked glycosylation occupancy by disrupting N-linked sequons. Interestingly, the two N-linked sequons in SARS-CoV-2 S directly impacted by variants, N0074 and N0149, are in divergent insert regions 1 and 2, respectively, of SARS-CoV-2 S in comparison with SARS-CoV-1 S (Figure 4A). The N0074, in particular, is one of the S glycans that interact directly with ACE2 glycan (at N546; Figure 7), suggesting that glycan-glycan interactions could contribute to the unique infectivity differences between SARS-CoV-2 and SARS-CoV-1. These sequon variants will also be important to examine in terms of glycan shielding that could influence immunogenicity and efficacy of neutralizing antibodies, as well as interactions with the host cell receptor ACE2. Naturally occurring amino acid-changing SNPs in the ACE2 gene generate a number of variants including one variant, with a frequency of three in 10,000 humans, that eliminates a site of N-linked glycosylation at N546 (Figure 6). Understanding the impact of ACE2 variants on glycosylation and more importantly on S binding, especially for N546S, which impacts the glycan-glycan interaction between S and ACE2 (Figure 7), should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation could lead to more potent biologics capable of acting as better competitive inhibitors of S binding."}

{"project":"LitCovid-sample-PD-FMA","denotations":[{"id":"T123","span":{"begin":790,"end":794},"obj":"Body_part"},{"id":"T124","span":{"begin":830,"end":840},"obj":"Body_part"},{"id":"T125","span":{"begin":867,"end":871},"obj":"Body_part"}],"attributes":[{"id":"A123","pred":"fma_id","subj":"T123","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A124","pred":"fma_id","subj":"T124","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A125","pred":"fma_id","subj":"T125","obj":"http://purl.org/sig/ont/fma/fma74402"}],"text":"Several emerging variants of the virus appear to be altering N-linked glycosylation occupancy by disrupting N-linked sequons. Interestingly, the two N-linked sequons in SARS-CoV-2 S directly impacted by variants, N0074 and N0149, are in divergent insert regions 1 and 2, respectively, of SARS-CoV-2 S in comparison with SARS-CoV-1 S (Figure 4A). The N0074, in particular, is one of the S glycans that interact directly with ACE2 glycan (at N546; Figure 7), suggesting that glycan-glycan interactions could contribute to the unique infectivity differences between SARS-CoV-2 and SARS-CoV-1. These sequon variants will also be important to examine in terms of glycan shielding that could influence immunogenicity and efficacy of neutralizing antibodies, as well as interactions with the host cell receptor ACE2. Naturally occurring amino acid-changing SNPs in the ACE2 gene generate a number of variants including one variant, with a frequency of three in 10,000 humans, that eliminates a site of N-linked glycosylation at N546 (Figure 6). Understanding the impact of ACE2 variants on glycosylation and more importantly on S binding, especially for N546S, which impacts the glycan-glycan interaction between S and ACE2 (Figure 7), should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation could lead to more potent biologics capable of acting as better competitive inhibitors of S binding."}

{"project":"LitCovid-sample-PD-GO-BP-0","denotations":[{"id":"T99","span":{"begin":70,"end":83},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T100","span":{"begin":763,"end":789},"obj":"http://purl.obolibrary.org/obo/GO_0051701"},{"id":"T101","span":{"begin":1004,"end":1017},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T102","span":{"begin":1083,"end":1096},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T103","span":{"begin":1354,"end":1367},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Several emerging variants of the virus appear to be altering N-linked glycosylation occupancy by disrupting N-linked sequons. Interestingly, the two N-linked sequons in SARS-CoV-2 S directly impacted by variants, N0074 and N0149, are in divergent insert regions 1 and 2, respectively, of SARS-CoV-2 S in comparison with SARS-CoV-1 S (Figure 4A). The N0074, in particular, is one of the S glycans that interact directly with ACE2 glycan (at N546; Figure 7), suggesting that glycan-glycan interactions could contribute to the unique infectivity differences between SARS-CoV-2 and SARS-CoV-1. These sequon variants will also be important to examine in terms of glycan shielding that could influence immunogenicity and efficacy of neutralizing antibodies, as well as interactions with the host cell receptor ACE2. Naturally occurring amino acid-changing SNPs in the ACE2 gene generate a number of variants including one variant, with a frequency of three in 10,000 humans, that eliminates a site of N-linked glycosylation at N546 (Figure 6). Understanding the impact of ACE2 variants on glycosylation and more importantly on S binding, especially for N546S, which impacts the glycan-glycan interaction between S and ACE2 (Figure 7), should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation could lead to more potent biologics capable of acting as better competitive inhibitors of S binding."}

{"project":"LitCovid-sample-GO-BP","denotations":[{"id":"T95","span":{"begin":70,"end":83},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T96","span":{"begin":763,"end":789},"obj":"http://purl.obolibrary.org/obo/GO_0051701"},{"id":"T97","span":{"begin":1004,"end":1017},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T98","span":{"begin":1083,"end":1096},"obj":"http://purl.obolibrary.org/obo/GO_0070085"},{"id":"T99","span":{"begin":1354,"end":1367},"obj":"http://purl.obolibrary.org/obo/GO_0070085"}],"text":"Several emerging variants of the virus appear to be altering N-linked glycosylation occupancy by disrupting N-linked sequons. Interestingly, the two N-linked sequons in SARS-CoV-2 S directly impacted by variants, N0074 and N0149, are in divergent insert regions 1 and 2, respectively, of SARS-CoV-2 S in comparison with SARS-CoV-1 S (Figure 4A). The N0074, in particular, is one of the S glycans that interact directly with ACE2 glycan (at N546; Figure 7), suggesting that glycan-glycan interactions could contribute to the unique infectivity differences between SARS-CoV-2 and SARS-CoV-1. These sequon variants will also be important to examine in terms of glycan shielding that could influence immunogenicity and efficacy of neutralizing antibodies, as well as interactions with the host cell receptor ACE2. Naturally occurring amino acid-changing SNPs in the ACE2 gene generate a number of variants including one variant, with a frequency of three in 10,000 humans, that eliminates a site of N-linked glycosylation at N546 (Figure 6). Understanding the impact of ACE2 variants on glycosylation and more importantly on S binding, especially for N546S, which impacts the glycan-glycan interaction between S and ACE2 (Figure 7), should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation could lead to more potent biologics capable of acting as better competitive inhibitors of S binding."}